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Hydrolase PDB id
2iar
Jmol
Contents
Protein chain
312 a.a. *
Metals
_CA ×2
Waters ×305
* Residue conservation analysis
PDB id:
2iar
Name: Hydrolase
Title: Crystal structure of squid ganglion dfpase w244h mutant
Structure: Diisopropylfluorophosphatase. Chain: a. Synonym: dfpase. Engineered: yes. Mutation: yes. Other_details: phosphotriesterase
Source: Loligo vulgaris. Organism_taxid: 6622. Organ: head ganglion. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Resolution:
1.90Å     R-factor:   0.196     R-free:   0.255
Authors: E.I.Scharff,J.Koepke,G.Fritzsch,C.Luecke,H.Rueterjans
Key ref:
E.I.Scharff et al. (2001). Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris. Structure, 9, 493-502. PubMed id: 11435114 DOI: 10.1016/S0969-2126(01)00610-4
Date:
08-Sep-06     Release date:   26-Sep-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q7SIG4  (DFPA_LOLVU) -  Diisopropyl-fluorophosphatase
Seq:
Struc: 		314 a.a.
312 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.1.8.2  - Diisopropyl-fluorophosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Diisopropyl fluorophosphate + H2O = diisopropyl phosphate + fluoride
Diisopropyl fluorophosphate
 + H(2)O
 = diisopropyl phosphate
 + fluoride
      Cofactor: Divalent cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biological_process   1 term 
  Biochemical function     hydrolase activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/S0969-2126(01)00610-4 Structure 9:493-502 (2001)
PubMed id: 11435114  
 
 
Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris.
E.I.Scharff, J.Koepke, G.Fritzsch, C.Lücke, H.Rüterjans.
 
  ABSTRACT  
 
BACKGROUND: Phosphotriesterases (PTE) are enzymes capable of detoxifying organophosphate-based chemical warfare agents by hydrolysis. One subclass of these enzymes comprises the family of diisopropylfluorophosphatases (DFPases). The DFPase reported here was originally isolated from squid head ganglion of Loligo vulgaris and can be characterized as squid-type DFPase. It is capable of hydrolyzing the organophosphates diisopropylfluorophosphate, soman, sarin, tabun, and cyclosarin. RESULTS: Crystals were grown of both the native and the selenomethionine-labeled enzyme. The X-ray crystal structure of the DFPase from Loligo vulgaris has been solved by MAD phasing and refined to a crystallographic R value of 17.6% at a final resolution of 1.8 A. Using site-directed mutagenesis, we have structurally and functionally characterized essential residues in the active site of the enzyme. CONCLUSIONS: The crystal structure of the DFPase from Loligo vulgaris is the first example of a structural characterization of a squid-type DFPase and the second crystal structure of a PTE determined to date. Therefore, it may serve as a structural model for squid-type DFPases in general. The overall structure of this protein represents a six-fold beta propeller with two calcium ions bound in a central water-filled tunnel. The consensus motif found in the blades of this beta propeller has not yet been observed in other beta propeller structures. Based on the results obtained from mutants of active-site residues, a mechanistic model for the DFP hydrolysis has been developed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21416312 S.Wellert, B.Tiersch, J.Koetz, A.Richardt, A.Lapp, O.Holderer, J.Gäb, M.M.Blum, C.Schulreich, R.Stehle, and T.Hellweg (2011).
The DFPase from Loligo vulgaris in sugar surfactant-based bicontinuous microemulsions: structure, dynamics, and enzyme activity.
  Eur Biophys J, 40, 761-774.  
19943158 J.Gäb, M.Melzer, K.Kehe, S.Wellert, T.Hellweg, and M.M.Blum (2010).
Monitoring the hydrolysis of toxic organophosphonate nerve agents in aqueous buffer and in bicontinuous microemulsions by use of diisopropyl fluorophosphatase (DFPase) with (1)H- (31)P HSQC NMR spectroscopy.
  Anal Bioanal Chem, 396, 1213-1221.  
20552250 J.G.Bogner-Strauss, A.Prokesch, F.Sanchez-Cabo, D.Rieder, H.Hackl, K.Duszka, A.Krogsdam, B.Di Camillo, E.Walenta, A.Klatzer, A.Lass, M.Pinent, W.C.Wong, F.Eisenhaber, and Z.Trajanoski (2010).
Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPARĪ³.
  Cell Mol Life Sci, 67, 4049-4064.  
20383004 M.M.Blum, S.J.Tomanicek, H.John, B.L.Hanson, H.Rüterjans, B.P.Schoenborn, P.Langan, and J.C.Chen (2010).
X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): perdeuteration of proteins for neutron diffraction.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 379-385.
PDB code: 3kgg
20329768 S.Chakraborti, and B.J.Bahnson (2010).
Crystal structure of human senescence marker protein 30: insights linking structural, enzymatic, and physiological functions .
  Biochemistry, 49, 3436-3444.
PDB codes: 3g4e 3g4h
18853398 J.M.Schmidt, M.J.Howard, M.Maestre-Martínez, C.S.Pérez, and F.Löhr (2009).
Variation in protein C(alpha)-related one-bond J couplings.
  Magn Reson Chem, 47, 16-30.  
19136630 M.M.Blum, M.Mustyakimov, H.Rüterjans, K.Kehe, B.P.Schoenborn, P.Langan, and J.C.Chen (2009).
Rapid determination of hydrogen positions and protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement.
  Proc Natl Acad Sci U S A, 106, 713-718.
PDB code: 3byc
18951406 X.Hu, X.Jiang, D.E.Lenz, D.M.Cerasoli, and A.Wallqvist (2009).
In silico analyses of substrate interactions with human serum paraoxonase 1.
  Proteins, 75, 486-498.  
17156125 J.R.Wu, J.H.Shien, H.K.Shieh, C.C.Hu, S.R.Gong, L.Y.Chen, and P.C.Chang (2007).
Cloning of the gene and characterization of the enzymatic properties of the monomeric alkaline phosphatase (PhoX) from Pasteurella multocida strain X-73.
  FEMS Microbiol Lett, 267, 113-120.  
18033585 J.Stöckigt, and S.Panjikar (2007).
Structural biology in plant natural product biosynthesis--architecture of enzymes from monoterpenoid indole and tropane alkaloid biosynthesis.
  Nat Prod Rep, 24, 1382-1400.  
  17183172 M.M.Blum, A.Koglin, H.Rüterjans, B.Schoenborn, P.Langan, and J.C.Chen (2007).
Preliminary time-of-flight neutron diffraction study on diisopropyl fluorophosphatase (DFPase) from Loligo vulgaris.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 42-45.  
17166853 Y.Tanaka, K.Morikawa, Y.Ohki, M.Yao, K.Tsumoto, N.Watanabe, T.Ohta, and I.Tanaka (2007).
Structural and mutational analyses of Drp35 from Staphylococcus aureus: a possible mechanism for its lactonase activity.
  J Biol Chem, 282, 5770-5780.
PDB codes: 2dg0 2dg1 2dso
16640555 G.Amitai, L.Gaidukov, R.Adani, S.Yishay, G.Yacov, M.Kushnir, S.Teitlboim, M.Lindenbaum, P.Bel, O.Khersonsky, D.S.Tawfik, and H.Meshulam (2006).
Enhanced stereoselective hydrolysis of toxic organophosphates by directly evolved variants of mammalian serum paraoxonase.
  FEBS J, 273, 1906-1919.  
15821095 D.P.Kloer, S.Ruch, S.Al-Babili, P.Beyer, and G.E.Schulz (2005).
The structure of a retinal-forming carotenoid oxygenase.
  Science, 308, 267-269.
PDB codes: 2biw 2bix
15593246 F.J.Stevens, C.Kuemmel, G.Babnigg, and F.R.Collart (2005).
Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: application.
  J Mol Recognit, 18, 150-157.  
15930621 J.Koepke, X.Ma, G.Fritzsch, H.Michel, and J.Stöckigt (2005).
Crystallization and preliminary X-ray analysis of strictosidine synthase and its complex with the substrate tryptamine.
  Acta Crystallogr D Biol Crystallogr, 61, 690-693.  
15098021 M.Harel, A.Aharoni, L.Gaidukov, B.Brumshtein, O.Khersonsky, R.Meged, H.Dvir, R.B.Ravelli, A.McCarthy, L.Toker, I.Silman, J.L.Sussman, and D.S.Tawfik (2004).
Structure and evolution of the serum paraoxonase family of detoxifying and anti-atherosclerotic enzymes.
  Nat Struct Mol Biol, 11, 412-419.
PDB code: 1v04
15190054 M.J.Maté, and C.Kleanthous (2004).
Structure-based analysis of the metal-dependent mechanism of H-N-H endonucleases.
  J Biol Chem, 279, 34763-34769.
PDB codes: 1v13 1v14 1v15
14646065 A.Fokine, R.Morales, C.Contreras-Martel, P.Carpentier, F.Renault, D.Rochu, and E.Chabriere (2003).
Direct phasing at low resolution of a protein copurified with human paraoxonase (PON1).
  Acta Crystallogr D Biol Crystallogr, 59, 2083-2087.  
12671655 E.Carafoli, and S.Ringer (2003).
The calcium-signalling saga: tap water and protein crystals.
  Nat Rev Mol Cell Biol, 4, 326-332.  
14501113 J.Koepke, E.I.Scharff, C.Lücke, H.Rüterjans, and G.Fritzsch (2003).
Statistical analysis of crystallographic data obtained from squid ganglion DFPase at 0.85 A resolution.
  Acta Crystallogr D Biol Crystallogr, 59, 1744-1754.
PDB code: 1pjx
  12547421 V.Anantharaman, L.Aravind, and E.V.Koonin (2003).
Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins.
  Curr Opin Chem Biol, 7, 12-20.  
  11937049 Z.Jawad, and M.Paoli (2002).
Novel sequences propel familiar folds.
  Structure, 10, 447-454.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.